LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 2.8636458 2.8636458 2.8636458 Created orthogonal box = (0.0000000 -50.582069 0.0000000) to (29.203571 50.582069 4.9599800) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4928571 4.5394165 4.9599800 Created 621 atoms using lattice units in orthogonal box = (0.0000000 -50.582069 0.0000000) to (29.203571 50.582069 4.9599800) create_atoms CPU = 0.002 seconds 621 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4928571 4.5394165 4.9599800 Created 626 atoms using lattice units in orthogonal box = (0.0000000 -50.582069 0.0000000) to (29.203571 50.582069 4.9599800) create_atoms CPU = 0.001 seconds 626 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 10 32 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 1246 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_343168101490_001#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 10 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.032 | 5.032 | 5.032 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5042.3072 0 -5042.3072 52691.717 66 0 -5325.3243 0 -5325.3243 2831.409 Loop time of 11.4863 on 1 procs for 66 steps with 1246 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5042.30715985839 -5325.31908639613 -5325.32433757892 Force two-norm initial, final = 374.54996 0.25076296 Force max component initial, final = 57.013224 0.052019463 Final line search alpha, max atom move = 1.0000000 0.052019463 Iterations, force evaluations = 66 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.44 | 11.44 | 11.44 | 0.0 | 99.60 Neigh | 0.025311 | 0.025311 | 0.025311 | 0.0 | 0.22 Comm | 0.011025 | 0.011025 | 0.011025 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009544 | | | 0.08 Nlocal: 1246.00 ave 1246 max 1246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5853.00 ave 5853 max 5853 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 120780.0 ave 120780 max 120780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120780 Ave neighs/atom = 96.934189 Neighbor list builds = 3 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 10 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.033 | 5.033 | 5.033 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -5325.3243 0 -5325.3243 2831.409 14653.537 68 0 -5325.351 0 -5325.351 -0.32198059 14677.592 Loop time of 0.506425 on 1 procs for 2 steps with 1246 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5325.32433757893 -5325.34944037636 -5325.35097131029 Force two-norm initial, final = 47.381234 0.48996741 Force max component initial, final = 37.983455 0.33397693 Final line search alpha, max atom move = 0.00017357970 5.7971615e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.50484 | 0.50484 | 0.50484 | 0.0 | 99.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028461 | 0.00028461 | 0.00028461 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001298 | | | 0.26 Nlocal: 1246.00 ave 1246 max 1246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5851.00 ave 5851 max 5851 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 120672.0 ave 120672 max 120672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120672 Ave neighs/atom = 96.847512 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 10 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.171 | 5.171 | 5.171 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5325.351 0 -5325.351 -0.32198059 Loop time of 2.31e-06 on 1 procs for 0 steps with 1246 atoms 173.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.31e-06 | | |100.00 Nlocal: 1246.00 ave 1246 max 1246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5849.00 ave 5849 max 5849 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 118080.0 ave 118080 max 118080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118080 Ave neighs/atom = 94.767255 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 10 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.171 | 5.171 | 5.171 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -5325.351 -5325.351 29.207436 101.20472 4.9654727 -0.32198059 -0.32198059 -25.218726 36.470876 -12.218092 2.3209222 725.87449 Loop time of 2.541e-06 on 1 procs for 0 steps with 1246 atoms 236.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.541e-06 | | |100.00 Nlocal: 1246.00 ave 1246 max 1246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5849.00 ave 5849 max 5849 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59040.0 ave 59040 max 59040 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 118080.0 ave 118080 max 118080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118080 Ave neighs/atom = 94.767255 Neighbor list builds = 0 Dangerous builds = 0 1246 -5325.35097131029 eV 2.32092223219497 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12